The military will continue to prosecute wars abroad but its troops will not get paychecks and civilian employees — possibly hundreds of thousands — face being sent home without pay, according to new guidance issued by the Defense Department in preparation for a partial government shutdown.

Deputy Defense Secretary Pat Shanahan sent out a memo with the guidance as Congress faces a looming midnight deadline when current government funding expires.

“The secretary and I hope that the Congress will pass a CR or an annual appropriations bill for defense activities during Fiscal Year 2018,” Shanahan wrote to the department.

But pay could become a major headache for troops and Defense Department civilians.

“Military personnel will not be paid until such time as Congress makes appropriated funds available to compensate them for this period of service,” Shanahan wrote.